When only a subset of all atoms is selected by the
model.pick_atoms() or model.pick_hot_atoms() commands (set 1), this
variable controls the interaction between the picked atoms and the rest of the
system. When it is 2 (default), the non-bonded pairs will contain only
selected atoms (set 1). This means that the optimized atoms will not ``feel''
the rest of the protein through the non-bonded terms at all.
If energy_data.nonbonded_sel_atoms is 1, only one of the atoms in
the non-bonded pair has to be a selected atom. This means that the selected
region feels the rest of the system through the non-bonded terms, at the
expense of longer CPU times. When all atoms are selected, this variable has
no effect.
